June 4, 2008

Please find appended the response of the Treatment Action Group (TAG) to NIAID’s “Request for Information (RFI): To Solicit Input and Ideas on Priorities in Basic Vaccine Discovery Research.” We would also refer you to TAG’s report from the Spring of 2000: “NIH-Funded AIDS Vaccine Research: A Critical Review,” by Gregg Gonsalves¹; the vast majority of the content remains as relevant today as it was at the time of publication. Of particular note, Gonsalves wrote: “It is of great concern to us that our findings and recommendations echo many of those made by researchers and advocates about the NIH AIDS vaccine program in the Levine report almost four years ago.”

In May of 2008, we can now also add that it is of great concern to TAG that many of our recommendations echo many of those made by TAG eight years ago, which in turn echoed those of the Levine Report almost four years prior to that. Given this observation, we hope that NIAID can understand why we greet this undoubtedly well-intentioned RFI with a certain amount of skepticism and cynicism.

It must also be stressed that the most pressing current need is to increase the NIH budget to address the net decline that has occurred over the past five years.

1. In which areas of basic vaccine discovery research should resources and emphasis be focused to solve the key scientific obstacles in HIV vaccine research?

1. Thorough analysis of efficacy trial data: HIV vaccine research can benefit greatly from the data obtained from clinical efficacy trials in humans. NIAID appears to have made little use of the data from the two largest efficacy trials conducted to date, the phase III studies of AIDSVAX. The principal investigators involved in these trials have made information and samples available to any investigator via a website: www.gsid.org/index.html.One obvious point of emphasis for basic discovery is, if possible, to analyze this large body of data to look for correlates of resistance and susceptibility to acquisition of HIV infection. A proposal for NIAID to support HLA typing of participants in this trial was not supported by the (then) AIDS Vaccine Research Working Group. Similarly, ongoing analyses of the data from the STEP/HVTN 502 trial are vital, and must be a key priority for support.
2. Animal resources: the shortage of macaques for vaccine & pathogenesis research is an overarching issue. The SHIV89.6P challenge virus — now much criticized — was initially employed because the consistency of CD4 depletion resulting from infection facilitated comparisons of vaccine effects in small groups of animals. While live attenuated SIV vaccines have the best track record in terms of achieving protection against SIV challenges in macaques, studies typically involve small numbers of animals, adding to the difficulty of evaluating correlates of immunity. Small numbers of macaques in vaccine experiments also increases the risk of confounding effects because they do not come close to reflecting the genetic diversity of a human trial population. Several recommendations from TAG’s 2000 report still hold:
   • “NIH needs to make greater resources available for animal-based research and to encourage a coordinated, rational approach to animal studies. The National Center for Research Resources (NCRR) has been negligent and unresponsive to criticisms from the Levine Committee and others regarding the administration of the Regional Primate Research Centers (RPRCs) and other primate colonies. NCRR should be catalyzing progress in this area rather than defending its bureaucratic turf.”
   • “Increase Resources per Research Study: Program staff at the National Institute for Allergy & Infectious Diseases (NIAID) and at NCRR need to direct additional funding to support studies with sufficient statistical power to offer reliable answers to research questions. Researchers should design studies to include larger numbers of primates (i.e., more than 3-4 per arm) and ask for this funding in their applications. Study sections need to look favorably on larger primate studies.”

   Furthermore, given concerns regarding attracting young investigators to the field, consideration should also be given to mechanisms to assist them in accessing animal resources.

3. Neutralizing antibodies: the generation of broadly neutralizing antibodies remains a key unrealized goal. The neutralizing antibody consortium convened by the International AIDS Vaccine Initiative (IAVI) continues to struggle with the development of systems for rapid screening and this is a key area for emphasis and resources. The controversy regarding the role of tolerance mechanisms in preventing the generation of broadly neutralizing antibodies is a worthy subject for a scientific workshop.
4. Correlates of protection in live attenuated vaccine studies: Live attenuated SIV vaccines remain the most successful immunogens for protecting macaques against SIV challenges (see above comment on animal resources). Efforts such as the live attenuated consortium sponsored by the IAVI need to be bolstered and expanded and NIAID should explore mechanisms to encourage and support data sharing among research groups working in this area.
5. Animal models of HIV acquisition: It has long been recognized that the risk of acquiring HIV infection from a single exposure is, in most cases, relatively low. Throughout the history of AIDS vaccine research, scientists have stressed the need to better model the acquisition of HIV infection in animal model systems. A number of repeated, low-dose challenge models have been developed but there is an urgent need to rigorously evaluate different approaches, understand the impact of potential confounding variables, and work toward a more standardized approach. The recent evidence that some vaccine vectors may enhance susceptibility increases the urgency of this issue, as it emphasizes the need to evaluate vaccine candidates for potential enhancement effects pre-clinically.
6. Exposure to virus during immunization: following on from the last point, there has recently been an increasing focus on conducting smaller phase IIb vaccine efficacy studies in high-risk populations. Participants in these studies are more likely to be exposed to HIV during the vaccination series. Animal model studies need to investigate the effects of exposure to virus at or around the time of immunizations, in order to better understand how this might affect acquisition of infection.
7. Making DNA vaccines immunogenic in humans: Given that vaccine vectors have components other than the HIV antigens they hope to provoke immune responses against, and may cause unpredictable adverse events, a renewed focus on enhancing the immunogenicity of DNA vaccines is needed. As with many of the issues highlighted here, animal shortages become an issue because a rigorous, standardized evaluation of DNA vaccines with multiple different candidate adjuvants is required to reveal the most promising approaches. Specific support for an initiative on DNA adjuvant design and research should be considered.
8. Optimizing the induction of T cell memory: A plethora of new tools have allowed scientists to track the development (differentiation) of memory CD4 and CD8 T cell responses to both vaccination and infection. Some functional properties, particularly the ability of a memory T cell to proliferate, have emerged as potentially important correlates of immunity. However, immunization schedules for T cell-based vaccines remain empirically based. An urgent priority should be to carefully track the differentiation of memory T cell responses to vaccine candidates (using technologies such as gene expression analysis in addition to functional and phenotypic markers) in order to ensure that immunization schedules are rational and do not risk compromising the function of a developing memory response by re-stimulating the responses prematurely. The Merck vaccine trial, for example started with immunizations a month apart. Recent data on Yellow Fever and Vaccinia vaccines clearly shows that CD8 T cell differentiation is ongoing at day 28 after immunization.²
9. Protecting developing CD4 T cell responses: Immunization involves the activation of CD4 T cells and their differentiation into memory CD4 cells. CD4 T cells undergoing this process have been shown to be “exquisitely sensitive” to HIV infection.³ To our knowledge, there has been essentially no effort to develop vaccine strategies that may help protect these responses from HIV infection should a recipient be exposed during an immunization series. Emphasis should be placed on addressing this issue, potentially through the use of adjuvants with direct anti-HIV properties and by evaluating whether the immune stimulation caused by specific vectors is conducive or hostile to HIV replication. More novel approaches could include combining vaccination with intermittent use of microbicides or pre-exposure prophylaxis in order to try and facilitate the development of anti-HIV responses without interference from exposure to HIV itself. As mentioned previously, this may be a particularly important in studies involving very high-risk populations. Emphasis should also be placed on evaluating the susceptibility of vaccine-induced CD4 T cell responses to HIV, with the goal of identifying methods that induce CD4 T cell phenotypes with the best ability to resist infection.
10. Improving the understanding of role of the HIV-specific CD4 response: Having been named the “helper” cell, the potentially critical role of CD4 T cell responses against has frequently been overlooked as if the name itself consigns the response to supportive and likely dispensable role. Yet HIV-specific CD4 responses have frequently emerged as correlates of viral load control, including in a recent therapeutic study of Merck’s now defunct adenovirus construct⁴ and in studies of live attenuated SIV vaccines.⁵ Emphasis and resources need to go into a detailed dissection of the role of CD4 responses, including breadth of targeting, function, resistance to HIV infection and the potential for HIV to develop escape mutations.
11. Standardization of polyfunctional T cell assays: A great deal of effort was put into standardizing the ELISpot assay for interferon gamma production, but the limitations of this approach (which may miss the majority of vaccine induced memory T cell responses in some cases⁶) have caused a shift toward assessing multiple functions (“polyfunctionality”). These assays also need to be standardized in terms of peptide concentrations, cut-offs for sensitivity etc. so that valid comparisons of the immunogenicity of different vaccine constructs can be made across trials.
12. Development of CD8 T cell killing assays: It has recently been highlighted that the peptide concentrations used in T cell assays may not give an accurate picture of the ability of a vaccine-induced CD8 T cell response to recognize and kill HIV-infected cells.⁷ Resources need to be put into the development and standardization of assays that better measure the killing ability of vaccine-induced T cells.
13. Induction of responses to multiple, diverse epitopes within each HIV protein: Disappointingly, Merck’s HIV vaccine induced T cell responses to an average of just one epitope in each vaccine-encoded protein. Evidence from both animal and human studies suggests that a much broader response is required, with responses to multiple epitopes within HIV’s Gag protein emerging as particularly important.^8,9 Methods for inducing responses to multiple epitopes within Gag and other proteins urgently need to be developed. Consideration should be given to evaluating combinations of multiple variants of the same protein (from both within HIV clades and from multiple clades). Similarly, the impact of different prime-boost vaccine approaches on the breadth of the resulting immune response requires careful study. These types of studies will also require additional support to facilitate the preparation of multiple, complex antigen combinations (the cost of which would likely be prohibitive under a traditional R01 grant).
14. Exploration of whole-killed vaccines in combinations: Also relating to breadth, the potential for developing whole-killed or equivalent mimics of near-complete HIV particles needs to be thoroughly evaluated and the criteria for assessing safety evaluated in partnership with the FDA. The current status of efforts to develop safe killed or equivalent vaccines should also be reviewed and the most promising approaches identified and selected for further evaluation. Such constructs should be studied both alone and in combination with other approaches in animal model studies.
15. Replicating vectors: Another longstanding issue with a profound regulatory aspect is the proposal that replicating vaccine vectors may offer advantages over non-replicating constructs. Current data is does not offer definitive support for this proposal, and additional animal model studies are needed. Developing vectors derived from live vaccines with a long safety record in humans, if possible, would be the logical priority.
16. Durable control of heterologous SIV challenge: Most SIV vaccine studies involve challenging animals with viruses containing the exact same proteins or epitopes that are used in the immunogen. Emphasis should be placed on also comparing efficacy against heterologous (non-matching) challenge viruses and evidence of efficacy against heterologous challenges should be a key requirement for advancing candidates into human efficacy testing.
17. Creation of multiple R5 SHIVs and comparisons with SIV: The SIV/HIV hybrid SHIV89.6P utilizes the CXCR4 co-receptor to gain entry into CD4 T cells and is clearly a poor choice of virus for most SIV/macaque challenge experiments. However, some studies indicate that SHIVs containing R5-using envelopes may more closely mimic HIV’s effects in humans. Only one R5-SHIV has seen limited use in challenge studies to date and additional variants should be developed and compared directly to SIV in vaccine/challenge experiments.
18. Standardized protocols for evaluation of impact of vector-specific immunity: The Merck trial highlighted unknowns regarding the impact of immune responses targeted against vaccine vectors. It would be helpful to develop recommendations for studying the impact of vector-specific immunity in animal models.
19. Non-elite long-term non-progressors (LTNP): We believe there is widespread consensus on the issue of studying exposed uninfected individuals and long-term non-progressors who control their viral loads to undetectable levels (“elite controllers”). NIAID should be supporting as many studies of these cohorts as possible. Individuals who maintain clinical & immunological health despite detectable or even high viral loads¹⁰ are also deserving of study. Dogma has developed that adaptive immune responses do not play a role in the similar phenomenon observed in naturally SIV-infected sooty mangabeys, but some researchers have challenged this interpretation¹¹ and recent evidence of transient immune activation and viral load peaks during acute SIV infection of mangabeys lends credence to this view.¹² Detailed analyses of the specificity and functional properties of virus-specific immune responses in both non-elite human LTNP mangabeys are needed and may improve our understanding of the correlates of immune protection.
20. Vaccine protection from immune activation: Following on from the last point, the strong association between immune activation and disease progression suggests that the markers of activation deserve evaluation in studies of vaccines designed to protect against AIDS as opposed to infection. Proposals to develop novel vaccines that might uncouple the typical correlation between viral load and immune activation should be considered.
21. Mucosal immunology: This technically challenging field is regularly cited as important to support, for very good reason. Knowledge in this area remains inadequate and NIAID, in addition to ensuring that grant proposals receive appropriate consideration, can play a role in facilitating ongoing dialogue between mucosal immunologists both within and outside of the HIV field.
22. Control immunizations: The correlations between antibody levels and resistance to HIV infection that emerged from the AIDSVAX trials¹³ led to the suggestion that vaccine trials should include control immunizations with irrelevant antigens to which participants had not previously been exposed (e.g. KLH). This issue of antibody levels as a marker of immune responsiveness deserves additional study, as others have recently argued.¹⁴
23. Role of non-neutralizing antibodies: Some scientists have argued that non-neutralizing antibodies may be able to play a role in protection via antibody-mediated cellular cytotoxicity. While data from the AIDSVAX trials offers no support for this claim,¹⁵ the potential for other immunogens to induce more effective non-neutralizing response still deserves exploration.
24. Gene therapies: Several scientists cite the promise of approaches that use gene therapy to generate persistent anti-HIV antibody responses. This promising area deserves support, but detailed, ongoing evaluations of safety, and ongoing dialogues with regulatory agencies regarding ultimate feasibility, is critical for these ideas to move beyond pipe dream status.
25. Innovation & novelty: Everyone would like to support innovative, novel ideas but it is not clear how such ideas should be defined. Ensuring adequate funding such that at least the top third percentile of investigator-initiated grants can be supported is the most critical factor for ensuring that new ideas are pursued.
26. Study sections: Study sections must also be fully appraised of the relevant priorities in AIDS vaccine research any of the suggestions resulting from this RFI are to come to fruition. While scientists at NIAID’s March 25 vaccine summit were repeatedly citing the importance of the breadth of the T cell response, at least one investigator was having a grant application addressing how to improve the breadth of vaccine-induced CD8 T cell responses turned down, on the basis that it’s not a relevant issue for human vaccines.

2. Which of these areas are best addressed through individual research projects and which through multi-disciplinary research teams?

As a general suggestion (in many cases either or approach might be considered):

Individual research projects: 6, 9, 12, 13, 14, 19, 20, 23, 24, 25

Multi-disciplinary research teams: 1, 2, 3, 4, 5, 7, 8, 10, 11, 15, 16, 17, 18, 21, 22

3. How can multidisciplinary research best be fostered to enhance the chance of successful outcomes?

A barren funding environment increases competition and decreases willingness to collaborate and share data.

Addressing that problem must be the #1 priority. Goal, priorities and roles need to be defined clearly ahead of time along with agreements regarding data presentation, publication, etc.

4. How can new investigators and new ideas from within and outside the HIV vaccine field best be attracted into these areas of research?

It would certainly helpful if the science of HIV infection generally, and HIV vaccine research specifically, could be conveyed accurately to the public. The coverage of NIAID’s March 25 vaccine summit is unlikely to have made the field seem appealing. Funding for training programs and pilot grants for young investigators are among many possibilities. An evaluation the extent to which the recommendations made in the 2005 IOM report “Bridges to Independence: Fostering the Independence of New Investigators in Biomedical Research” have been implemented should be considered. NIAID is in a unique position to sponsor cross-disciplinary workshops where basic scientists working outside of the field can interact with those within. The implementation of two or three such workshops annually on different topics related to vaccine research could help sustain dialogues better than one-off events.

TAG strongly encourages NIAID to convene a specific meeting to discuss questions 3 & 4.

1. NIH-Funded AIDS Vaccine Research: A Critical Review.
2. Miller JD, van der Most RG, Akondy RS, et al. Human effector and memory CD8(+) T cell responses to smallpox and yellow Fever vaccines. Immunity. 2008 May;28(5):710-22. Epub 2008 May 8. HIV-specific CD4+ T cells. Nature. 2002 May 2;417(6884):95-8.
3. Douek DC, Brenchley JM, Betts MR, et al. HIV preferentially infects HIV-specific CD4+ T cells. Nature. 2002 May 2;417(6884):95-8.
4. Schooley R, Wang H, Spritzler J et al. Therapeutic Vaccination with a Replication Defective Adenovirus Type 5 HIV-1 gag Vaccine in a Prospective, Double-blinded, Placebo-controlled Trial (ACTG 5197). Abstract #87, CROI, Boston 2008
5. Gauduin MC, Yu Y, Barabasz A, et al. Induction of a virus-specific effector-memory CD4+ T cell response by attenuated SIV infection. J Exp Med. 2006 Nov 27;203(12):2661-72. Epub 2006 Nov 20.
6. De Rosa SC, Lu FX, Yu J, Perfetto SP, et al. Vaccination in humans generates broad T cell cytokine responses. J Immunol. 2004 Nov 1;173(9):5372-80.
7. Bennett MS, Ng HL, Ali A, Yang OO. Cross-clade detection of HIV-1-specific cytotoxic T lymphocytes does not reflect cross-clade antiviral activity. J Infect Dis. 2008 Feb 1;197(3):390-7.
8. Rolland M, Heckerman D, Deng W, et al. Broad and Gag-biased HIV-1 epitope repertoires are associated with lower viral loads. PLoS ONE. 2008 Jan 9;3(1):e1424.
9. Goepfert PA, Lumm W, Farmer P, et al. Transmission of HIV-1 Gag immune escape mutations is associated with reduced viral load in linked recipients. J Exp Med. 2008 May 12;205(5):1009-17. Epub 2008 Apr 21.
10. Choudhary SK, Vrisekoop N, Jansen CA, Otto SA, Schuitemaker H, Miedema F, Camerini D. Low immune activation despite high levels of pathogenic human immunodeficiency virus type 1 results in long-term asymptomatic disease. J Virol. 2007 Aug;81(16):8838-42. Epub 2007 May 30.
11. Wang Z, Metcalf B, Ribeiro RM, McClure H, Kaur A. Th-1-type cytotoxic CD8+ T-lymphocyte responses to simian immunodeficiency virus (SIV) are a consistent feature of natural SIV infection in sooty mangabeys. J Virol. 2006 Mar;80(6):2771-83.
12. Estes JD, Gordon SN, Zeng M, et al. Early Resolution of Acute Immune Activation and Induction of PD-1 in SIV-Infected Sooty Mangabeys Distinguishes Nonpathogenic from Pathogenic Infection in Rhesus Macaques. J Immunol. 2008 May 15;180(10):6798-807.
13. Gilbert PB, Peterson ML, Follmann D, et al. Correlation between immunologic responses to a recombinant glycoprotein 120 vaccine and incidence of HIV-1 infection in a phase 3 HIV-1 preventive vaccine trial. J Infect Dis. 2005 Mar 1;191(5):666-77. Epub 2005 Jan 27.
14. Moore JP, Klasse PJ, Dolan MJ, Ahuja SK. A STEP into darkness or light? Science. 2008 May 9;320(5877):753-5.
15. Karnasuta C, Paris RM, Cox JH et al. Antibody-dependent cell-mediated cytotoxic responses in participants enrolled in a phase I/II ALVAC-HIV/AIDSVAX B/E prime-boost HIV-1 vaccine trial in Thailand. Vaccine. 2005 Mar 31;23(19):2522-9.